After the death of his father Biju Patnaik, leader of the Janata Dal,[12] he was elected as a member to the 11th Lok Sabha in the by-election from Aska Parliamentary Constituency in Odisha, India.[12] He was a member of the Consultative Committee of Ministry of Steel & Mines, Member of Standing Committee on Commerce, and Member Library Committee of Parliament. A year later the Janta Dal split and Patnaik founded the Biju Janta Dal which in alliance with the BJP-led National Democratic Alliance (NDA) performed well and Patnaik was selected the Union Minister for Mines in the cabinet of A.B.Vajpayee. However, as the BJD won the majority of seats in alliance with the BJP in the Odisha Assembly elections, Patnaik resigned from the Union cabinet and was sworn in as the Chief Minister of Odisha in 2000.

BJP led NDA lost the general elections in 2004, however the coalition led by Naveen Patnaik emerged victorious in the state legislative elections and he continued as the Chief Minister.During this tenure, the friction between the ruling partners was getting more and more apparent, especially after the killing of Swami Laxmanananda Saraswati[14] in the Kandhamal district of Odisha in 2007–2008 and also active participation of Bajrang Dal in the riots that hit Kandhamal region.

In the run-up to the polls for the Lok Sabha and Legislative Assembly of Odisha elections in 2009, BJD walked out of the NDA after severing ties with the BJP and joined the nascent Third Front constituted mainly by the Left Front and few regional parties.[15] He did it after severely criticising BJP's involvement in Kandhamal anti-Christian riots during 2007. The BJD won a resounding victory in both the Vidhan Sabha (State Assembly) as well as the Lok Sabha elections in 2009, winning 14 out of 21 Lok Sabha seats and 103 of the 147 assembly seats and was sworn in as the Chief Minister of Odisha on 21 May 2009 for the third consecutive term.[16]

Patnaik spent most of his early days away from Odisha, so he couldn't learn the Odia language. He is the only chief minister of India who does not speak the regional language of the state and because of this he has been facing severe criticism from his opponents. However, he possesses great mastery over the Hindi, French and English. At rallies, he delivers Odia speeches written in Roman alphabet.[18]

Some MP, MLAs of Patnaik's party BJD have been accused of involvement in chit fund scam and questioned by the CBI in 2014.[19][20][21] CBI is investigating over 30 companies in relation to these multi-crore financial scams, which have robbed lakhs of the state's poor of their lifetime savings. Questions were raised because of Patnaik's silence over this issue and his proximity to many such businesses, as he was photographed at the launch of a news channel by one such company.[22]